Contacts of the strand formed by residues 230 - 239 (chain A) in PDB entry 3H90
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 230 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A THR* 6.1 1.8 - - - -
228A VAL* 4.3 6.8 - - - +
229A SER* 1.3 82.6 + - - +
231A ALA* 1.3 58.4 + - - +
249A LEU* 3.8 1.0 - - - -
250A GLU* 2.7 50.8 + - - +
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Residues in contact with ALA 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A VAL* 3.6 30.3 - - + -
223A THR* 5.1 11.8 - - + +
228A VAL* 5.4 0.2 - - + -
230A GLY* 1.3 75.0 - - - +
232A HIS* 1.3 63.1 + - - +
247A ILE* 3.9 13.7 - - + -
248A HIS 3.1 13.9 - - - +
249A LEU* 4.2 2.0 - - + -
250A GLU* 3.6 3.0 + - - +
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Residues in contact with HIS 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A ALA* 1.3 74.6 - - - +
233A ASP* 1.3 74.6 + - + +
234A LEU* 3.6 5.4 + - - +
247A ILE* 4.6 1.4 - - - +
248A HIS* 2.9 26.1 + + + +
250A GLU* 3.0 28.0 + - + +
285A ASP* 2.7 17.7 - - + -
289A VAL* 3.7 22.7 - - + +
293A ZN 1.9 37.8 - - - -
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Residues in contact with ASP 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A HIS* 1.3 85.3 - - + +
234A LEU* 1.3 60.8 + - - +
235A ARG* 2.7 51.7 + - - +
246A GLN* 3.5 1.5 - - - +
247A ILE* 2.8 29.0 - - - +
248A HIS* 3.1 32.4 + - + +
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Residues in contact with LEU 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A ARG* 3.7 40.8 - - + +
218A ILE* 3.9 23.8 - - + -
219A ILE* 4.8 10.8 - - + -
232A HIS 3.6 5.1 + - - +
233A ASP* 1.3 75.9 + - - +
235A ARG* 1.3 65.2 + - - +
236A THR* 4.1 13.2 + - + -
245A ILE* 4.0 13.9 - - + -
246A GLN 3.2 15.5 - - - +
247A ILE* 4.0 20.2 - - + -
72C SER* 4.5 5.5 - - - -
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Residues in contact with ARG 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A ASP* 2.7 44.6 + - - +
234A LEU* 1.3 72.6 - - - +
236A THR* 1.3 63.9 + - - +
244A PHE 3.7 0.7 - - - +
245A ILE* 3.5 4.3 - - - -
246A GLN* 2.9 57.5 + - + +
72C SER* 3.6 37.3 + - - +
73C PHE* 3.5 26.2 - - + +
244C PHE* 4.3 9.1 - - - -
279C ASP* 2.4 43.4 + - - -
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Residues in contact with THR 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A ASP 4.5 0.3 - - - +
208A ARG 3.9 0.5 - - - +
209A ALA* 3.4 23.5 + - - +
210A LEU* 3.4 41.3 + - + +
215A ARG* 4.4 11.8 + - + +
218A ILE* 4.1 17.0 - - + -
234A LEU* 4.1 18.1 + - + +
235A ARG* 1.3 81.3 - - - +
237A ARG* 1.3 68.0 + - - +
244A PHE 3.3 5.4 - - - -
245A ILE* 4.1 7.4 - - + -
72C SER* 3.5 9.6 + - - -
73C PHE* 3.8 5.0 - - - -
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Residues in contact with ARG 237 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A PHE* 4.0 24.4 - - - +
77A LYS* 4.7 2.4 - - - +
207A ASP* 3.4 37.3 + - + +
208A ARG 3.5 17.3 - - - +
209A ALA* 4.6 0.9 - - - +
210A LEU* 4.2 7.5 - - - +
236A THR* 1.3 78.8 - - - +
238A GLN* 1.3 58.3 + - - +
239A SER* 5.1 2.6 - - - -
243A ARG* 3.4 4.0 - - - +
244A PHE* 2.6 76.5 + - + +
246A GLN* 5.4 2.8 - - - +
73C PHE* 3.6 25.9 - - + -
207C ASP* 2.7 29.3 + - - -
237C ARG* 3.7 22.1 - - - +
246C GLN* 5.8 0.2 - - - +
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Residues in contact with GLN 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A LYS* 4.6 2.5 - - - -
143A GLN* 6.4 0.2 - - - +
204A SER* 4.4 21.7 - - - +
207A ASP* 5.3 0.3 - - - +
208A ARG 4.4 3.2 + - - -
210A LEU* 3.5 14.9 - - + +
211A PRO* 4.8 3.3 - - - +
214A GLU* 4.1 4.0 - - - +
237A ARG* 1.3 78.8 - - - +
239A SER* 1.3 60.3 + - - +
240A GLY 3.2 22.9 + - - +
241A PRO* 3.3 14.3 + - - +
242A THR 3.4 13.7 - - - +
243A ARG* 3.4 33.6 + - + +
244A PHE* 4.4 2.2 - - - +
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Residues in contact with SER 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A PHE* 6.4 0.2 - - - -
74A GLY* 4.2 10.2 + - - -
76A GLY* 3.6 18.8 + - - -
77A LYS* 3.8 35.2 - - - +
204A SER* 6.3 0.2 - - - -
237A ARG* 5.1 3.8 - - - -
238A GLN* 1.3 70.8 - - - +
240A GLY* 1.3 65.0 + - - +
241A PRO* 3.1 5.4 - - - +
242A THR* 3.0 21.8 + - - +
244A PHE* 3.6 22.5 - - - -
207C ASP* 5.2 0.7 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il